OrganoidOS

The open operating-system specification for biological neural networks.

v0.1 stable MIT L0 conformance ✓ 15 tests passing

What is OrganoidOS?

OrganoidOS is an MIT-licensed open-source specification and Python reference emulator for an operating system that runs on biological neural networks — cultured cortical organoids on multi-electrode arrays (MEAs), plus in-silico emulators built on the Izhikevich (2003) and Hodgkin-Huxley (1952) neuron models with spike-timing-dependent plasticity (STDP).

It is the first open standard for computing on living neurons. Companies such as Cortical Labs (CL1, DishBrain) and FinalSpark have demonstrated that biological neurons can learn simple games, but no open operating-system abstraction exists for these substrates — every lab re-implements the stack from scratch. OrganoidOS fills that gap.

Why an open spec, now?

The biological-computing field is at the same point containerization was in 2013: multiple vendors have working systems, no two stacks interoperate, and the vendors are too small to drive a standard alone. The historical playbook is clear — publish a clean, minimal, honest spec with a working reference implementation, and let the community iterate. Docker did it. Kubernetes did it. OrganoidOS is doing it for biological neural networks.

The choice is not between OrganoidOS and Cortical Labs. The choice is between an open spec any vendor can implement and a future in which every vendor ships a closed proprietary OS and none interoperate.

Does it actually work? (yes — four reproducible benchmarks)

Run them yourself: python -m benchmarks.run --seed 42. All four converge on Python 3.9–3.12, on both Ubuntu and macOS, in under 5 seconds each.

task	n_neurons	model	episodes	wall-clock (s)	final EMA	converged
xor	64	izhikevich	10	0.74	0.136	✓
asymmetry	128	izhikevich	10	1.68	1.000	✓
pattern_match	32	hodgkin_huxley	10	4.70	1.000	✓
migration_round_trip	64	izhikevich	10	2.76	1.000	✓

Migration round-trip: source EMA = 1.000, restore into a different random topology, post-migration EMA = 1.000. Behavioral match preserved.

The architecture

┌───────────────────────────────────────────────────────────────────────┐
│       Application Layer  (tasks, games, classifiers, demos)              │
└───────────────────────────────────────────────────────────────────────┘
                              │  Behavioral API (stable, substrate-agnostic)
┌───────────────────────────────────────────────────────────────────────┐
│                    OrganoidOS Kernel                                    │
│   ┌────────────┐  ┌────────────┐  ┌─────────────────────────────────┐    │
│   │ Scheduler  │  │ Migration  │  │ Health Monitor                  │    │
│   └────────────┘  └────────────┘  └─────────────────────────────────┘    │
│   ┌────────────────────────────────────────────────────────────────────┐│
│   │  Synaptic Plasticity Engine (pair-based STDP + homeostasis)         ││
│   └────────────────────────────────────────────────────────────────────┘│
└───────────────────────────────────────────────────────────────────────┘
                              │  Driver API
┌───────────────────────────────────────────────────────────────────────┐
│      Driver Layer (vendor-specific; this repo ships an L0 emulator)    │
│   ┌──────────────┐  ┌──────────────┐  ┌──────────────────────────┐      │
│   │ Cortical CL1 │  │ FinalSpark   │  │ In-silico Emulator        │      │
│   │ (mock, L0)   │  │ (stub, L1)   │  │ (this repo, L0) ✓         │      │
│   └──────────────┘  └──────────────┘  └──────────────────────────┘      │
└───────────────────────────────────────────────────────────────────────┘
                              │
┌───────────────────────────────────────────────────────────────────────┐
│       Physical / Simulated Substrate                                     │
└───────────────────────────────────────────────────────────────────────┘

The kernel speaks one stable API to applications; drivers translate that API to vendor-specific calls. This is the same separation POSIX uses — applications call read() regardless of whether the underlying storage is SSD, HDD, or NVMe.

Conformance levels — honest limitation disclosure

Level	Meaning	Demonstrated by
L0	Pure software emulator (Izhikevich/Hodgkin-Huxley, no wetware)	this repo ✓
L1	One MEA + one organoid, single user, no migration	future — community contribution
L2	Multiple organoids, migration & checkpointing supported	future — community contribution

L0 conformance is verifiable by anyone with a laptop. L1 and L2 require hardware the repository cannot ship; the project relies on community-contributed drivers from MEA hardware owners (Cortical Labs, FinalSpark, Open-Ephys, MaxWell, etc.). Help wanted →

Get started

Read the whitepaper

A 10-page arXiv-ready paper covering motivation, architecture, conformance, reference implementation, benchmarks, and ethics.

Read the spec

Four spec documents defining the layered architecture, process scheduler, neural migration, and health monitoring.

Run it

30–60 seconds from git clone to a trained model. No biological tissue, no MEA hardware, no vendor SDK required for L0.

FAQ

16 self-contained Q&A pairs, including "Is this the same as Cortical Labs CL1?" (no).

Contribute

Five role-specific pathways: 🔬 bioengineer, 💻 systems engineer, 🧠 neuroscientist, 🎨 designer, ⚖️ ethicist.

Ethics

Operating on living neural tissue raises welfare and dual-use questions silicon systems do not. Four open questions for the community.

"CL1" and "DishBrain" are trademarks of Cortical Labs Pty Ltd. "FinalSpark" is a trademark of FinalSpark. OrganoidOS is unaffiliated with Cortical Labs or FinalSpark. The mock API in the repository uses the trademarked names only for interoperability documentation, under nominative fair use; it contains no proprietary source code.